Spec
PigeonholeFinderPigeonhole-based finder. Must be used together with PigeonholePattern.
Pigeonhole-based finder. Must be used together with PigeonholePattern.
Extends | Finder |
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All Extended | Finder |
Defined in | <seqan/index/find_pigeonhole.h> |
Signature |
template <typename THaystack, typename TSpec>
class Finder<THaystack, Pigeonhole<TSpec> >;
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Template Parameters
TSpec |
Specifies the type of pigeonhole filter. |
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THaystack |
The type of the sequence that should be searched. Types: ContainerConcept |
Interface Function Overview
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THitString getWindowFindHits(finder);
Returns the string of hits from the finder. -
windowFindBegin(finder, pattern, errorRate)
Initializes the pattern. Sets the finder on the begin position. Gets the first non-repeat range and sets it in the finder. Used together with windowFindEnd. -
void windowFindEnd(finder, pattern);
Flushes the pattern. Used together with windowFindBegin and windowFindNext. -
bool windowFindNext(finder, pattern, finderWindowLength)
Searches over the next window with the finder. The found hits can be retrieved with getWindowFindHits Used together with windowFindBegin and windowFindEnd.
Interface Functions Inherited From Finder
Member Typedef Overview
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typedef (...) PigeonholeFinder::THitString;
The type to use for the hit string returned in getWindowFindHits.
Detailed Description
Provides a fast filter algorithm that uses the pigeonhole lemma, i.e. if a pattern matches with k errors in the text, every partition into k+1 parts contains one part that matches without error.
The Pattern must be a q-gram index over multiple patterns. The tolerated error rate must be given when find or windowFindBegin is called. In these functions the length of the index Shape is set automatically thus it must be modifiable at runtime, e.g. OneGappedShape.
See Also
Interface Functions Detail
THitString getWindowFindHits(finder);
Returns the string of hits from the finder.
Parameters
finder
|
A PigeonFinder. |
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Returns
THitString |
String of Hits, see THitString. |
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Data Races
Thread safety unknown!
See Also
windowFindBegin(finder, pattern, errorRate)
Initializes the pattern. Sets the finder on the begin position. Gets the first non-repeat range and sets it
in the finder. Used together with windowFindEnd.
Parameters
finder
|
The PigeonholeFinder to use. |
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pattern
|
The PigeonholePattern to use. |
errorRate
|
Error rate that is allowed between reads and reference. Should be the same in as in windowFindNext. Types: double |
Data Races
Thread safety unknown!
See Also
void windowFindEnd(finder, pattern);
Flushes the pattern. Used together with windowFindBegin and windowFindNext.
Parameters
pattern
|
A pattern with window interface. |
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finder
|
A finder with window interface. Types: PigeonholeFinder |
Data Races
Thread safety unknown!
See Also
bool windowFindNext(finder, pattern, finderWindowLength)
Searches over the next window with the finder. The found hits can be retrieved with getWindowFindHits Used together with windowFindBegin
and windowFindEnd.
Parameters
finder
|
The PigeonholeFinder to use. |
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pattern
|
The PigeonholePattern to use. |
finderWindowLength
|
Number of bases that are scanned beginning from the position the finder is at. Including bases that are marked as repeats and that are skipped. Types: unsigned. |
Returns
bool |
true, if there are bases that can be scanned, false otherwise. |
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Data Races
Thread safety unknown!
See Also
Member Typedef Detail
typedef (...) PigeonholeFinder::THitString;
The type to use for the hit string returned in getWindowFindHits.